Fallout Rise of the Mentor
by Dreximus0000
Summary: While living in Vault 101, John had made many discoveries that no one else knew. When forced to leave the vault he does not go through the front entrance but on a vessel that was hidden from everyone. Join John as he searches for his father and tries to bring stability and justice to the Capital.
1. Chapter 1

Chapter 1: Discovery, Escape, and Prepare for the rise of The Army of Chaos.

A/N Co-Authored by _LTcrazy2_

A/N I do not own anything except the plot and the right to play god with these peoples lives.

"Speech"

 _'Thought'_

 _"Telepathy"_

 _ **"Communications"**_

 **"A.I./Robot"**

2070: An unusual aircraft carrier appears just outside Washington D.C. Once it was boarded it was discovered no on was onboard and all systems were not operating. A few months later it was moved to a top secret underground cavern near to where vault 101 was.

2257: During an experiment, an accident causes Catherine to be exposed to multiple forms of energy. No problems were detected after this but it was discovered that she was a few weeks pregnant.

2258: John Shepard was born to James and Catherine. After James wife dies in childbirth James cancels the project and heads to vault 101.

2263: It is discovered by James and his friend Jonas discover that John was affected by the energy that Catherine was exposed to. He displayed extremely heightened intelligence, his senses were extremely sharp.

2268: On his tenth birthday, John receives his first pip-boy. He is also excited to begin his first job in the vault which is helping out engineering.

2269: While sorting through storage in a forgotten part of the vault, John comes across an armored door. Judging by the amount of dust gathered everywhere no one has been here possibly since the vault was constructed. Using his pip-boy to open the door with the override function, he enters to explore the long hallway that seemed not to end.

Once he reached the end of the corridor he enters through another door into a large underground facility. Finding a light switch he brings on the lights only to see a huge technological cavern with what seems to be a modified aircraft carrier.

2270: Over the last year, John has made numerous trips to the cavern and the aircraft carrier which he discovered was actually called a helicarrier which appeared outside DC two hundred years ago but no one could figure any of it out except to put information into it which now gave John access to pre-war information.

2271: Utilizing the helicarrier's systems and manufacturing capabilities, John built two new pip-boys more advanced than the one he had to wear in the vault. This new model included a digital storage system allowing his to carry anything he wanted with him and never need a bag to carry it such as weapons and such.

2274: John passes the G.O.A.T. and begins full work in the engineering section. This was also the year John and Amata Almodovar started dating.

2276: By this time John had made the lives of all within vault 101 better. He had optimized the reactor to increase its energy production and made the hydroponics and hydro-reclamation systems four times more efficient. But most importantly to himself he had finally activated the main computer core for the Helicarrier. An A.I. was onboard that spoke to him months ago identifying itself in a feminine voice as Skynet. He could remember that day as he had so many questions.

 _*Flashback*_

 _John was walking through the helicarrier trying to find out everything he could. Just as he was gonna call it a day he came across a room with a glowing panel. Walking up to it he touch's the panel and a blue glowing feminine face appears. "Greetings. Who are you?"_

 _John was shocked for a moment before answering. "My name is John Shepard. What are you?"_

 _The hologram looked at him closely before answering. "I am Skynet. The A.I. that helps control this helicarrier."_

 _John now understood a little as to why the pre-war scientists couldn't get into the system. "Why are you activating now? I read logs from the holotapes that pre-war scientists tried to get info from the computers but only succeeded in storage all the worlds info into them before the bombs fell."_

 _Skynet looked at john and then had a thoughtful look before responding. "To answer that question I need some information. First what is the year?"_

 _John looked at his pip-boy to make sure and then answers. "The year is 2276."_

 _Skynet looks at John in a confused manner before answering. "Allow me to properly introduce myself. I am Skynet, the ultimate A.I. developed in concert with this helicarrier by Strategic Homeland Intervention Enforcement and Logistics Division and Strategic Homeland Division in 2016. Though my records show that this is an entirely different universe as I can not detect S.H.I.E.L.D. or SHD satellites."_

 _John decided to try looking through files while talking to Skynet with only some luck. "Why are some files locked?"_

 _Skynet processed the inquiry while also looking into the files in the core. "Director Fury of_ S.H.I.E.L.D. and Director Louis Chang of SHD made provisions for any and all situations the helicarrier would find itself in. At this moment you can only access systems and items that will help your world but not anything that will cause more destruction than has already happened. As this seems to be a different reality than my origin I can only manufacture items your world has created that are in my files and give them upgrades. The files are also very dangerous as no expense was spared to research, design, and develop this helicarrier and all technology in the files."

*End Flashback*

2277: John's father opened the vault and left without telling him. But instead of going out the front door he made his way to the cavern after saving his girlfriend Amata from security but also spared the overseer since he was her father.

Present

John ran up to the helicarrier after making sure that no one could ever get through the corridor without his express permission. Moving through is her heard Skynet. **"John, what is going on?"**

Once on the bridge John answered. "My father left the vault and the overseer decided to make me a scapegoat. Can we move the helicarrier out of here?"

The hologram for Skynet appeared before him. **"Yes. The retractable roof is not functioning. But if I bring the engines online and active the chronosphere we can appear in the air above D.C."**

John nodded. "What about people seeing us? I don't think people will respond well to a flying aircraft carrier."

Skynet could see where he was going. **"The retro-reflective panels which can make the ship invisible only work for a short time before needing to recharge. It will be enough until a suitable alternative can be found. Also since I assume you will be following your father on the ground I can offer the teleporter system to allow you in and out of the helicarrier when you need to restock."**

John liked this idea as he saw the files for what she was talking about. "Very well. Bring engines online and charge up the chronosphere and retro-reflective panels. We are leaving the vault for the capital wasteland."

The helicarrier repulsor engines were brought online and began to lift the helicarrier from its cradle. John could feel the ship vibrate and the blasting force of the engines. Looking around he saw a chair between four consoles and decided to sit there as that seemed to be where the ship commander would sit.

Once seated, holographic screens popped up showing status reports and the systems of the helicarrier. Everything looked good and all systems he had access to were functioning.

As the helicarrier made it to the very center of the cavern, the chronosphere was used to chronoshift above the clouds where the retro-reflective panels were activated. Once everything evened out he stood and looked around. His eyes hurt for a few seconds are they adjusted to the bright natural light. Once he could see clearly again he moved to the window and looked down at the capital wasteland. "Okay. Now that we are out I have no idea what to do first."

Skynet appeared next to him. **"Might I make a suggestion?"**

John looked at Skynet "By all means. All I know is I need to find where my father went."

Skynet brought up a map of the entire capital wasteland going out 100 kilometers in all directions. **"Based on the radio signals and details my sensors are picking up, the capital wasteland has many problems that a well equipped person could help with."**

John was a little confused by this. "Such as?"

Skynet now bright up a strange structure. **"This is the town of megaton close to vault 101. You could start your journey there and see where it leads you. This could help you in your search for your father and see what you can do to help the inhabitants. I would also suggest before starting that you build yourself some armor and weapons from the database to suit your needs."**

John could see the potential in this as his journey to find his dad would require him to make as many allies as he could. "Very well. I will head to the manufacturing bay to start on my weapons and armor."

In the manufacturing bay John tried to figure out what he would like as his weapons. His pip-boy alpha's could hold all the ammunition he would ever need but reloading a weapon would take time. "Skynet. Is there a holographic display in here?"

His question was answered by a hologram appearing before him. **"This system will allow you to select and modify weapons based on my origins and this worlds. It will also allow you to fabricate armor. Though if you are going to use power armor you should use the simulation system to train in how to wear and utilize it. Synthesizers onboard are working to create more materials for you to use and you can use the matter converter to break down scrap into more materials. This will respond to vocal commands as well."**

John began with his armor. "Okay. Lets go with sturdy combat armor." Sturdy combat armor showed up in a boring tan color that was not flattering. "Lets start with the color. Black with the vault-tec symbols. Place retractable full-spectrum goggles into the helmet and slim it down a little and place a highly-encrypted comm system in so that I can keep in contact with the helicarrier. Place these round energy shields in the gauntlets. Make the outside a Kevlar-plastic polymer. Underneath that make it this hardened, compressed, lightweight titanium alloy."

The hologram changed to match his orders and he liked what he saw. "Very good, fabricate." With that the armor fabricators went to work showing construction time being seventy-two hours.

John then moved over to the weapons holograms.

John began looking at the holographic weapons before making decisions. "Lets make two deliverers with marksman's grips, extended clips and reflex sight and keep the silencer." The hologram changed to show his weapons to his specifications. "Begin build and start new weapon." Again he watched the hologram change and weapon fabricators begin work that would last twelve hours.

"Next is the sniper rifle. color is black. Set for variable zoom, marksman's stock, cushion grip, .50 caliber receiver, large quick eject magazine, long ported barrel, and a large muzzle break with it being able to swap with a suppressor. begin building." Estimated time twenty four hours.

John looked at mid-range weapons. "Select P90, black, reflex sight, suppressor, cushion grip, with full-auto and semi-auto selections. Build." Estimated time thirty six hours.

John now looked into melee weapons in case he has people getting close to him. "Lets make a couple Katana. Folded steel. Laser sharpened blades. I want an adjustable setting for the blade to be coated in electricity. Place a microfusion breeder cell in the handle for power requirements. Begin build." The timer showed twelve hours until completion.

Looking at ammo next he decided to prepare for anything. "Also begin construction on ammo. .50 caliber and 10mm. All large quick eject magazines. Lets start with five hundred clips per gun. Two hundred for basic ammo. One hundred for incendiary ammo. One hundred for explosive ammo. and one hundred for shredder ammo. begin build." The timer appeared for twelve hours.

Walking over to the last station which made robots he decided a robotic companion would be useful. "Lets make a few robots for carrying the stuff I collect and for other uses around the capital."

Looking at the selections he made his decision. "The floating eyebots will work. One repair, one medical, and one scout, the scout will need to be modified with an upgraded stealth boy and transmitter so I can see what it sees through my pip-boys. All eyebots should be made with the same titanium alloy as my armor and enhance their thrusters to increase hover and flight speed when necessary and give each a light laser gun for defense and offense. Equip the repair eyebot with a repair beam emitter and the medical eyebot with a minor regeneration beam emitter. Begin construction." Estimated time was fifty-six hours.

John took a minute to look through all the files in the system with a cursory glance before turning to Skynet. "Skynet, If you are not doing anything else at times please look into researching and developing anything else that may be of use for any situations. Also begin construction of a nanocore. I have a feeling I will need it soon.

Skynets hologram popped up after this. **"Very well. Nanocore calibration will take six hours. Might I also suggest going through the genetic modifier. Based on your experience, exposures, and environment you can modify your genetics to provide increases in your abilities."**

John nodded at this and made his way to the medical bay where he found the genetic modifier. It looked like a bed in the middle of a circle of holographic screens. This made sense as modifications would need a person to sleep while they took affect. Laying down in the bed the screens came to like with words and numbers.

 **This system takes your experiences, DNA and environment you will be moving through into consideration when modifying your genetic structure. The SPECIAL system will allow for increases within a point system you have earned. Other perks and abilities will be mapped from your genetics and the world itself.**

 **SPECIAL points available 3**

 **Strength: 6**

 **A measure of your raw physical power.**

 **Perception: 9**

 **A measurement of your environmental, situational, and spatial awareness pertaining to all your senses.**

 **Endurance: 6**

 **A measure of your overall physical fitness.**

 **Charisma: 6**

 **Your ability to charm and convince others.**

 **Intelligence: 15**

 **A measure of your overall mental acuity.**

 **Agility: 6**

 **A measure of your overall finesse, reflexes, and speed.**

 **Luck: 6**

 **A measure of your general good fortune.**

 **Can unlock two abilities.**

 **Biotic abilities available:**

 **Biotic barrier(Locked)**

 **Biotic Sense(Locked)**

 **Tech Powers Available:**

 **Tactical Cloak(Locked)**

 **Tech armor(Locked)**

 **Perk Points 5**

John looked at all the stuff available before making selections. "Unlock Biotic sense. Put points into strength, luck and charisma. For perks select swift learner, rad resistance, chem resistance. While I am undergoing these changes I will use the simulator to go over any information about the immediate area.

Leaning back in the bed he nodded off to sleep from the anesthetic allowing the mental simulator to let him learn while unconscious. Skynet watched as John would most likely be the one to help the capital wasteland know peace. But that was just her opinion.


	2. Chapter 2: Journey Beginning

Chapter 2: Journey Beginning

A/N Co-Authored by _LTcrazy2_

A/N I do not own anything except the plot and the right to play god with these peoples lives.

"Speech"

 _'Thought'_

 _"Telepathy"_

 _ **"Communications"**_

 **"A.I./Robot"**

*Four days later*

John Shepard woke up feeling refreshed and changed. He got up and began to put on the clothes laid out for him. As he put them on he could already tell the changes he selected had taken hold. His biotic sense allowed him to instinctively tell the mass and movement of things around him.

Once dressed he spoke. "Skynet. What is our current status?"

A hologram sprung up before him. **"Your combat armor, dual deliverer's, P90, Sniper rifle, Katana's and ammo have finished fabrication and are placed in the armory on the central table. Nanocore calibration is complete. If you require the nanocore it will scan the area and be able to build any additions people will want. Also as a precaution I have added kinetic shield emitters to your armor and the eyebots."**

John nodded at this. "What are these kinetic barriers?"

Skynets hologram changed to a simulation. **"Kinetic barriers provide protection from ballistic damage for a small amount of time before they need to recharge. Bullets, shrapnel and other projectiles will be nullified while the barrier is up. However the system will require you to swap out a microfusion cell every so often as needed to power the device. 100 microfusion cells have been manufactured for your use. That should provide plenty of power for the kinetic barriers. A warning though. While ballistics are blocked, energy based damage will bypass 50% of the shield allowing you protection just not as much as against bullets."**

Again John nodded in understanding. "Very well. While I am away please continue scanning and research and development. I want to know what we can do to help out there and if you can find where my father went as well."

Skynets hologram nodded. **"Of course. The teleporter is prepared to drop you just outside the cave housing Vault 101. Which is where you would have appeared if you had used the vault door. Also before you leave an additional note, the repair eyebot has the capability to unlock locked containers and safes, however you do have some paperclips stored on your pip-boy if you wish to handle it yourself at times."**

Nodding and clicking on his pip-boy, a flash of blue light and John was heading out to help the wasteland, and find his dad.

He teleported directly outside the cave for vault 101 as this is where a vault dweller would have come from. He checked his gear once more before pulling out his P90 and slapping a clip of normal rounds into it and setting off to the decimated town he saw a little ways away.

His HUD on his goggles made notes of everything that he was seeing. Walking through the ruins of Springvale he saw destroyed houses, radiation in the background, even sensing life. He walked slowly through town as he didn't know what to expect. His every step seemed to echo in the early morning with no one around.

Looking around the place he found mailboxes and containers, some filled with items he could use but mostly the area was filled with trash and scraps.

Before he could head towards a town seemingly called Megaton, his pip-boy picks up a radio broadcast which seemed to be a distress signal. Tuning to the frequency he listened in.

 _ **"This is Defender Morrill. Any Outcasts listening on this frequency report to sector 7-B, Bailey's Crossroads. This is a high-priority message; backup is needed at our location. Any personnel listening on this frequency, please report at once."**_

Clicking on his pip-boy he opened a frequency with Skynet. "Skynet. Can you locate the source of that transmission?"

Skynets avatar appeared on the screen. _**"I have the location now. Sending coordinates to your pip-boy as well as directions to get there. It seems you will have to go through a metro tunnel to get there."**_

John nodded. "Good. I will head to that location and try to help these outcasts. Maybe we will get more information on the capital wasteland from them."

Signing off the frequency, John headed to the location designated on his pip-boy. He moved at a steady pace to keep from tiring, but also to get there with as much haste as he can. Once he made it to the metro tunnels, he came across his first feral ghoul which went down quickly from a few headshots.

Seeing that they were unarmored he swapped his normal ammo for shredder rounds. Picking up the pace he came across more ferals, a few took more than a few hits to go down, he figured they had more resistance to damage due to mutation.

Making his way outside the metro and up stairs to the street. He noticed many people in what looked like power armor fighting tall green creatures that were shotting at them. Moving over to one of the armored people he slid and hid behind the same barricade before he heard the person speak. "Who the hell are you civilian?"

John frowned a little at the disgust in her voice. "Name is John Shepard. Maybe you can not be such a bitch to those who are answering your distress transmission."

He could hear the frown in her voice when she spoke again. "What does a civilian think they can do here to help?"

In response he checked his ammo for the P90 to make sure he had a full clip of shredders. After seeing a full clip he jumps over the barricade and immediately shoots the green creatures advancing on his position. As they wore minimal armor, the shredder rounds went through them with ease. His excellent marksmanship also allowed him to get majority of headshots killing those ones quickly before moving onto other targets.

30 seconds in and 14 of the creature lay dead from his weapon. During the silence he reloaded a fresh clip and looked to the outcasts. "That's what a fucking civilian can do."

Not bothering to wait, he sprinted forward towards the transmissions source cutting down any super mutants, which is what Skynet has told him they are, with ease making the outcasts seem inefficient and useless. When he made it to the transmission source, he was escorted down an elevator to meet with their leader.

Once the door opened they were greeted by Defender Morrill who was instantly verbally aggressive. "Great, another dirty civilian."

John took offense. "This dirty civilian just saved your comrades asses out there, so loose the attitude and be thankful."

Defender Morrill looked insulted but didn't respond except to make John follow him to his leader.

They reached an office where his superior apparently was. "Here's the person you wanted to see. I still don't think we need his help."

Protector McGraw cut him off. "That's enough. Return to your post."

Defender Morrill saluted and left.

Protector McGraw turned to John. "Sorry about that, we're all getting a little antsy from being here for so long. I could actually use your help with that."

Looking around John recognized the facility for what it was from historical records in vault 101. "You need me to help you get through the operation anchorage simulation to open a vault that's tied to it yes?"

McGraw looked surprised by that. "How do you know about that?"

John smiled. "Vault 101 has extensive historical records on military installations and labs."

McGraw nodded. "So will you help us?"

John looked him straight in the eyes. "I will, on the condition that once the vault is open I be allowed to scan anything inside with my pip-boys. Any physical technology is yours for the taking."

McGraw and John shook hands and headed for the simulator room.

A/N Please read and review.


End file.
